According to a report from The Register, the performance of web apps saved to / launched from the home screen of iOS-powered devices running iOS 4.3 is significantly lower than the performance offered by the same web apps, when launched directly via Mobile Safari.
While at this stage, it is unclear whether Apple purposely decided to degrade the performance of these web apps or not, early tests show that web apps are not able to take full advantage of the device’s hardware, as opposed to native apps.
The Register found out that a web app launched from the home screen under iOS 4.3 runs more than twice as slow as the same app launched from Safari. Apple did not fully acknowledge the issue, but it would appear that the new Nitro JavaScript engine featured in iOS 4.3 is not available for web apps launched from the home screen. According to the news outlet, “Essentially, there are two different JavaScript engines. […] They’re not using the new JavaScript engine with applications that launch from the home screen.” To add insult to injury, these web apps are not allowed to leverage HTML5 web caching, to prevent them from running offline.

Still according to The Register, developers have already filed bug reports with Apple in order to solve the issue, and Apple only partially acknowledged the difference in performance. Note that while parts of the issue are currently being addressed by Apple, the Cupertino-based company does not plan to bring the performance of web apps launched from the home screen to the performance level enjoyed by the same apps running under Mobile Safari.
While it is too early to come to conclusions, several developer believe that the crippled performance could be intentional, in order to favor native iOS apps over web apps.